Data Quality Assessment Report

massqc from tidymass by Xiaotao Shen

2022-03-06


INTRODUCTION

massqc (version 0.01): Created in 2021 by Xiaotao Shen


PARAMETERS

Table 1: Parameter setting

pacakge_name function_name parameter time
massprocesser process_data path:~/scratch60/CRC RPLC POS 2022-03-02 12:25:08
massprocesser process_data polarity:positive 2022-03-02 12:25:08
massprocesser process_data ppm:20 2022-03-02 12:25:08
massprocesser process_data peakwidth:5,30 2022-03-02 12:25:08
massprocesser process_data snthresh:10 2022-03-02 12:25:08
massprocesser process_data prefilter:3,500 2022-03-02 12:25:08
massprocesser process_data fitgauss:FALSE 2022-03-02 12:25:08
massprocesser process_data integrate:2 2022-03-02 12:25:08
massprocesser process_data mzdiff:0.01 2022-03-02 12:25:08
massprocesser process_data noise:500 2022-03-02 12:25:08
massprocesser process_data threads:6 2022-03-02 12:25:08
massprocesser process_data binSize:0.025 2022-03-02 12:25:08
massprocesser process_data bw:5 2022-03-02 12:25:08
massprocesser process_data output_tic:FALSE 2022-03-02 12:25:08
massprocesser process_data output_bpc:FALSE 2022-03-02 12:25:08
massprocesser process_data output_rt_correction_plot:FALSE 2022-03-02 12:25:08
massprocesser process_data min_fraction:0.5 2022-03-02 12:25:08
massprocesser process_data fill_peaks:FALSE 2022-03-02 12:25:08
massdataset create_mass_dataset() no:no 2022-03-02 14:50:02
massdataset mutate() parameter_1:batch=as.character(batch) 2022-03-06 09:18:52

SAMPLE INFORMATION

#> -------------------- 
#> massdataset version: 0.99.9 
#> -------------------- 
#> 1.expression_data:[ 14585 x 298 data.frame]
#> 2.sample_info:[ 298 x 6 data.frame]
#> 3.variable_info:[ 14585 x 3 data.frame]
#> 4.sample_info_note:[ 6 x 2 data.frame]
#> 5.variable_info_note:[ 3 x 2 data.frame]
#> 6.ms2_data:[ 0 variables x 0 MS2 spectra]
#> -------------------- 
#> Processing information (extract_process_info())
#> create_mass_dataset ---------- 
#>       Package         Function.used                Time
#> 1 massdataset create_mass_dataset() 2022-03-02 14:50:02
#> process_data ---------- 
#>         Package Function.used                Time
#> 1 massprocesser  process_data 2022-03-02 12:25:08
#> mutate ---------- 
#>       Package Function.used                Time
#> 1 massdataset      mutate() 2022-03-06 09:18:52

Figure 1: Peak intensity profile.


MISSING VALUES


MISSING VALUES IN DATASET

Black is MV.

Figure 2: Missing values in dataset


MISSING VALUES IN VARIABLES

Figure 3: Missing values in variables


MISSING VALUES IN SAMPLES

Figure 4: Missing values in samples


RSD DISTRIBUTATION

Figure 5: RSD distributation


INTENSITY FOR ALL THE VARIABLES

Figure 6: Intensity for all the variables


SAMPLE CORRELATION

Figure 7: Sample correlation


PCA score plot

Figure 7: PCA score plot